Can't view FTP uploaded files

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1

Have files in ftp upload directory. Galaxy Can’t see them. Galaxy log output is as follows:

galaxy.webapps.galaxy.api.remote_files WARNING 2020-03-18 14:24:38,692 [p:40699,w:1,m:0] [uWSGIWorker1Core4] Could not get ftp files: directory (/Dedicated/resgalproddata/database/ftp/brian-ring@uiowa.edu) is a symlink to a location not on the whitelist
Traceback (most recent call last):
File “/Dedicated/resgalaxyprod/lib/galaxy/webapps/galaxy/api/remote_files.py”, line 103, in index
response = self.__load_all_filenames(user_ftp_dir, trans.app.config.user_library_import_symlink_whitelist)
File “/Dedicated/resgalaxyprod/lib/galaxy/webapps/galaxy/api/remote_files.py”, line 118, in __load_all_filenames
if self.__safe_directory(directory, whitelist=whitelist):
File “/Dedicated/resgalaxyprod/lib/galaxy/webapps/galaxy/api/remote_files.py”, line 169, in __safe_directory
raise exceptions.ConfigDoesNotAllowException(‘directory (%s) is a symlink to a location not on the whitelist’ % directory)
ConfigDoesNotAllowException: directory (/Dedicated/resgalproddata/database/ftp/brian-ring@uiowa.edu) is a symlink to a location not on the whitelist

ftp related galaxy.yml info:

ftp_upload_dir: /Dedicated/resgalproddata/database/ftp
ftp_upload_site: research-galaxy.iihg.uiowa.edu
ftp_upload_dir_identifier: email
ftp_upload_dir_template: ‘${ftp_upload_dir}/${ftp_upload_dir_identifier}’
user_library_import_symlink_whitelist: /Dedicated/resgalproddata/database/ftp/

2

This can be closed, Solution:

resgalproddata was a mount point on a different filesystem. To keep things consistent the data dir was symlinked in the galaxy server directory by the admin who built the Galaxy instance. This allowed extra space for uploads.

I had assumed the error in the log file was related to the user directory created by ftp. Didn’t realize things were linked higher up in the filetree until I did a >df -h and noticed the large directory was a seperate filesystem.